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Table 2 Bacterial findings and contribution of different methods to diagnostic yield in the study population

From: Etiology of community-acquired pneumonia and diagnostic yields of microbiological methods: a 3-year prospective study in Norway

Pathogen No. (%) of patients with positive findings(n = 267) Blood culture(n = 267) Pleural fluid culture(n = 14) Urinary antigen test(n = 262) BAL(n = 8) Sputum sample for culture and/orL. pneumophilaPCR(n = 165)a NP swab culture(n = 263) PCR Serology(n = 263)
NP swab(n = 262)b OP swab(n = 262)c
Streptococcus pneumoniae 81 (30) 21 - 24 - 4 10 6 16 NA
Bordetella pertussis 15 (6) NA NA NA NA NA NA - - 15
Haemophilus influenzae 14 (5) 1 - NA - 5 8 NA NA NA
Mycoplasma pneumoniae 10 (4) NA NA NA NA NA NA 7 1 2
Chlamydophila pneumoniae 7 (3) NA NA NA NA NA NA - 2 5
Legionella pneumophila 7 (3) NA NA 7 NA - NA NA NA NA
Enterobacteriaceae d 6 (2) 2 - NA - 3 1 NA NA NA
Moraxella catarrhalis 5 (2) - - NA - 2 3 NA NA NA
Miscellaneous e 3 (1) 1 1 NA - - 1 NA NA NA
Haemophilus parainfluenzae 2 (1) 1 - NA - 1 - NA NA NA
Totalf 126 (47) 26 1 31 - 15 23 13 19 22
  1. Note: Data are number of patients, unless otherwise stated, whose infections were etiologically established by use of a particular method listed in descending order of specificity (NP vs. OP swab PCR depends on pathogen tested). Additional patients had etiology established by use of different methods; e.g., S. pneumoniae infection was established by use of urinary antigen test in 24 additional patients whose etiology was not established by use of blood culture etc. PCR: S. pneumoniae was detected by use of qPCR; and L. pneumophila, M. pneumoniae, C. pneumoniae and B. pertussis by use of real-time PCR. BAL, bronchoalveolar lavage; qPCR, real-time quantitative polymerase chain reaction; NP, nasopharynx; OP, oropharynx; NA, not applicable.
  2. aOf 165 sputum samples, 73 were of good quality. One of these tested positive for L. pneumophila by use of real-time PCR (urinary antigen test in this case was also positive).
  3. bOf 262 patient samples, 240 revealed valid results for qPCR detection of S. pneumoniae, and 259 for real-time PCR detection of M. pneumoniae, C. pneumoniae and B. pertussis.
  4. cOf 262 patient samples, 238 revealed valid results for qPCR detection of S. pneumoniae, and 259 for real-time PCR detection of M. pneumoniae, C. pneumoniae and B. pertussis.
  5. dInclude either of the following: E. coli, P. aeruginosa or Enterobacter species.
  6. eBlood culture, Group A streptococcus; Pleural fluid culture, Prevotella spp. and Dialister pneumosintes (isolated from the same patient); NP swab culture, Group A streptococcus.
  7. fNo. of patients does not add up to no. of pathogens because some patients had multiple pathogens detected: a total of 150 bacteria were detected in 126 patients.